It's important to add \label after a numbered element e.g. That's a tough one... you are right, there is a somewhat inconsistent behavior of textformat=empty depending if you place the label inside or not: Well, I certainly hope the caption package can "fix" it. Have a question about this project? We are using a few more chunk options as well. LaTeX by default recognizes \"table\" and \"figure\" floats, but you can define new ones of your own (see Custom floats below). Compiled with texmath 0.8.4, highlighting-kate 0.6. Notebook document is a special format of HTML document that render to html each time it is save. Already on GitHub? Figure labels are generated from knitr, and knitr only generate raw LaTeX code for figures in certain cases (including the ones you mentioned): https://github.com/yihui/knitr/blob/89b34a661c78beb1012584025a56008c7712f181/R/hooks-md.R#L7-L13 In other cases, it generates Markdown ! The marker can be seen as a name that we give to the object that we want to reference. I'm not sure if this can be even fixed within the caption package: The caption's argument would have to be executed without being typeset. By clicking “Sign up for GitHub”, you agree to our terms of service and http://tex.stackexchange.com/q/20816/9128. The first, p1b, is just a label that allows us to refer to it by name. We’ll occasionally send you account related emails. Figure 6.4 shows what a figure looks like in the main column. Define size in YAML header. Figures. knitr is an engine for dynamic report generation with R. It is a package in the programming language R that enables integration of R code into LaTeX, LyX, HTML, Markdown, AsciiDoc, and reStructuredText documents. It will be nice for the caption package to fix it, and I do not see the point of using \ref{} when there are no captions or caption numbers under the figures (e.g. 4.7 Cross-referencing within documents. I would like to ask to re-open this issue because it is affecting me considerably and I do think the problem extends beyond the latex package caption. At the … I think the answer by Andrew Stacey suggests that placing \label outside \caption for interoperability with the showlabels package. Make sure you have knitr and kfigr installed, use devtools::install_github("github mkoohafkan/kfigr") to install kfigr: 3. Tables are not quite so easy, but the ability to produce fully reproducible tables is really important. Anyway, since more than one person has reported this problem, I guess I'll make the change anyway. On my system, removing only textformat=empty fixed the issue. You should never be copy-pasting or retyping data summaries into a table. The text was updated successfully, but these errors were encountered: Do you have a reference for this? Cross-referencing is a useful way of directing your readers through your document, and can be automatically done within R Markdown. However if you leave fig.retina blank in your R chunk it will apply the default rmarkdown … Sign up for a free GitHub account to open an issue and contact its maintainers and the community. 6.2.4 Main column figures. We will explain how to use other packages and functions later in this section. Thank you for any help on this and also for the excellent knitr tool ;-). These options are given by LaTeX’s figure environment. The label of a figure environment is generated from the label of the code chunk, e.g., if the chunk label is foo, the figure label will be fig:foo (the prefix fig: is added before foo). []() and Pandoc will convert Markdown to LaTeX. The author of caption is active on TeX.SX, so we might get response from there. A side note: I was thinking about a similar problem, just the other way round: Adding figure captions to Markdown -> HTML output. Default settings for images and figures are taken from both the knitr and rmarkdown packages. to your account. This is the default type of figures in the LaTeX/HTML output, and requires no special chunk options. Have a question about this project? And the fact is that all my references to the figures created with knitr are missed because of this "awkward" style of putting the label inside of the caption (I agree with the opinions expressed in the above SE post that putting it outside is more conventional and readable). One of the small problems I faced was adding labels to pictures. Contribute to yihui/knitr-examples development by creating an account on GitHub. To put the \label outside of \caption wouldn't it be enough to change line 124 of file hooks-latex.R from: @ltorgo Yes, it probably takes 10 seconds for me to make that change. You may try the bookdown package (https://bookdown.org), and the output format bookdown::pdf_document2. I don't know if moving \label outside breaks other things. Currently, referencing figures and tables in knitr documents is a bit difficult. There is an SE post: http://tex.stackexchange.com/q/20816/9128 but it did not really tell if one should use one style or the other. If you think you have found something related to this, please open a new issue by following the issue guide (https://yihui.org/issue/), and link to this old issue if necessary. Successfully merging a pull request may close this issue. knitr require unique label for chunk. to your account. However, you can look up precisely how all the figures have been generated and, with a single command, re-create the manuscript (with all figures and supplementary data) after you changed a parameter. using fig.env puts \label{...} inside \caption{...} like this: this is not recommended, \label{} should be after \caption{} like this: the label can get lost using the latex package caption and calling \captionsetup{}. The filename of figure files is the combination of options fig.path and label.This function returns the path of figures for the current chunk by default. \section, \subsection, \captionetc, otherwise the label won't "latch on" to the correct number or counter. Floats are there to deal with the problem of the object that won't fit on the present page, and to help when you really don't want the object here just now.Floats are not part of the normal stream of text, but separate entities, positione… 14.7 Use knitr::knit_expand() to generate Rmd source; 14.8 Allow duplicate labels in code chunks (*) 14.9 A more transparent caching mechanism. As you cannot render with duplicated label, it cannot be save. The knitr source code shows a default value of 1 for fig.retina. From my understanding, both should work then, and I routinely put the \label just with the caption text in my documents. Besides margin and full-width figures, you can certainly also include figures constrained to the main column. If you think you have found something related to this, please open a new issue by following the issue guide (https://yihui.org/issue/), and link to this old issue if necessary. when you say "see Figure 1" but there is no "Figure 1" in the document). R version 3.2.1. Figure labels and figure environment not working in Rmarkdown -> pdf. This chunk of code can take some extra parameters to customize the dynamic output. A collection of knitr examples. The key issue is not the change itself, but why some LaTeX packages or classes do not work when \label{} is inside \caption{}. While this has been explained in Chapter 2 from the bookdown book, we want to present a brief summary below.. To use cross-references, you will need: Let's see an example: As you see, the text in between the characters <<>>= and @is R code, this code and its output is printed in a listing-like format. Figures are really easy in knitr. This prints the number assigned to the object labeled by marker. Changing this might be fine (I'd have to update my test cases, though), but I'm reluctant to do it. Hmm, but surely the figure caption should work even if the label does not? In this section, we discuss how to add figures and tables into your rmarkdown document, and how to provide captions for them. Documents that contain R code must be saved with the extension .Rtex, otherwise the code won't work. For now, the most convenient way to generate a table is the function knitr::kable(), because there are some internal tricks in knitr to make it work with bookdown and users do not have to know anything about these implementation details. Already on GitHub? Labeling the chunk gives us control the plot’s filename, which turns out to be “Rnw-filename-label.pdf” (Rnw is a Sweave file extension). Next we are using the option fig.pos="H", this tells knitr to include it with a certain position. The figure caption should work, but the chunk option is fig.cap instead of fig.caption. Figures are super easy in knitr. Also change \ref{fig:pressure} to \@ref(fig:pressure). Then we set a height for the figure as well as giving it a caption. privacy statement. Sign up for a free GitHub account to open an issue and contact its maintainers and the community. I'm writing a book for Wiley and they have a Latex "Wiley Data Mining Style" where they internally define the captions. Since no other drawbacks have been mentioned, and there seems to be a problem with @dr-moebius's example -- shouldn't knitr really do the same? For example both packages include a default setting for fig.retina. In case you prefer the figures not to have the filename of your source-file, there is a Sweave option that globally controls the figure-filename-prefix and the directory to which they are saved: I would like to plot 2 figures side-by-side using knitr. ok, than this is probably a bug of the caption package, here is a minimum working example: Could you please double-check your LaTeX output? You signed in with another tab or window. For LaTeX, one can embed \\label{the-label} in the caption, but Markdown seems to be unsupported. Sign in For chunks in your doc that produce a figure or table for which you want a caption, be sure to include a label in the chuck options line. This prints the number of the page where the object labeled by markerappears. Using knitr version 1.13.1, installed from github, the following document fails to create a figure environment with caption and label: --- title: "Untitled" output: pdf_document: fig_caption: yes --- Figure \ref{fig:pressure}. You signed in with another tab or window. The text was updated successfully, but these errors were encountered: I don't think this ever worked for R Markdown before. We take some data first: data (mtcars) names (mtcars) ## [1] "mpg" "cyl" "disp" "hp" "drat" "wt" "qsec" "vs" "am" "gear" ## [11] "carb" Not let’s plot. privacy statement. And the fact is that all my references to the figures created with knitr are missed because of this "awkward" style of putting the label inside of the caption (I agree with the opinions expressed in the above SE post that putting it outside is more conventional and readable). For example, the first chunk is this doc has the label number_figures 4. One point of particular interest is the sizing of figures. The purpose of knitr is to allow reproducible research in R through the means of Literate Programming.It is licensed under the GNU General Public License. Although I'm by no means a Latex expert to understand it, I can assure you that they do not use either the caption package or the \captionsetup command. To reference a figure, use the syntax \@ref(label) , 6 where label is the figure label, e.g., fig:foo . Successfully merging a pull request may close this issue. Description. By clicking “Sign up for GitHub”, you agree to our terms of service and In knitr: A General-Purpose Package for Dynamic Report Generation in R. Description Usage Arguments Value Note Examples. This old thread has been automatically locked. Thanks! This old thread has been automatically locked. It seems quite standard, or am I misunderstanding something? View source: R/utils.R. 9 Figures, Tables, Captions.. You need figures and tables in your own writing, whether it be a journal paper, an internal document, or some documentation. We’ll occasionally send you account related emails. I get: \caption[this is the caption of fig1]{this is the caption of fig1\label{fig:fig1}}, sorry, it must be \ref{fig:fig1} i changed it in the example, and then the same without \captionsetup{}, in the second example the reference works right, in the first it does not, because the \captionsetup command messes it up, i thought it was a wrong to place the label inside caption, the question is who to blame knitr or caption ;-). I know I could use par(mfrow=c(1,2)), but I've done a lot of work making the figures just right as they are. Sign in As you can see, the caption ends up at the bottom of the figure. If a setting exists in both packages the rmarkdown value will be used. 1.15.2 Floats are containers for things in a document that cannot be broken over a page. I actually had already downloaded the github source and made the change locally, and was able to confirm that this solves my problem ;-). 2.5 Tables. Using knitr version 1.13.1, installed from github, the following document fails to create a figure environment with caption and label: pandoc version: See the next section. The documentation of the caption package reads: So you have to place the \label command either just after or inside the caption text (mandatory argument of \caption). Let’s look at some ways how to size a figure with RMarkdown. Personally I'm more comfortable with the label inside caption. Both packages the rmarkdown value will be used an SE post: http: but. I would like to plot 2 figures side-by-side using knitr to our terms of service and statement. \Label just with the label wo n't  latch on '' to the main column the captions or data... If I can do it today R Markdown of caption is active on TeX.SX, so we might get from. That placing \label outside breaks other things that render to HTML each time it is save figures, don... 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